package main;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.NoSuchElementException;

import org.biojava.bio.BioException;

import utils.SequenceDatabase;
import utils.Driver;
import utils.Permutator;
import utils.SequenceDriver;

public class ShufflingMain {
	private final static String permFile = "permutations5";

	public static void main(String[] args) throws NoSuchElementException,
			BioException, IOException {
		SequenceDatabase db = new SequenceDatabase("sequences/LSURef93_lbl.fasta");
		
		System.out.println("Number of LSU organisms: "
				+ db.size());
		Permutator p = new Permutator(5, "sequences/" + permFile);

		SequenceDriver d = new SequenceDriver(db, new FileInputStream(new File("sequences/"
				+ permFile)), "sequences/outputShuffled.csv");

		System.out.println("Program finished");
	}
}
